In this study, we measured diastolic septal perforator flow velocities by Doppler transthoracic echocardiography (TTE) in patients with hypertrophic cardiomyopathy (HCM). Using color-guided pulsed Doppler TTE, septal perforator flow velocity recordings were attempted in 69 patients and successfully recorded in 47 (68%). First, we compared 14 patients with HCM to 12 controls and to 11 patients with hypertension with left ventricular hypertrophy. Next, in 10 additional patients with HCM, we compared the septal velocities with the epicardial left anterior descending artery (LAD) velocities recorded during the same TTE study. In the patients with HCM, the peak septal diastolic velocities were twice that of the normal controls (88 +/- 40 vs 41 +/- 13 cm/s) and also higher than in hypertensive left ventricular hypertrophy (51 +/- 18 cm/s, p < 0.0001). All 10 patients with HCM showed a step-up of peak diastolic velocity from the LAD to the septal perforator from 41 +/- 9 to 72 +/- 17 cm/s (p < 0.0001). Three patients with HCM had surgical septal myectomy. These patients had luminal narrowings of the small intramural arteries at histopathologic examination. In conclusion, pulsed Doppler measurement of septal perforator flow velocities is feasible. In HCM, the epicardial coronary arteries enlarge to accommodate increased flow, and diastolic velocity is normalized. In contrast, the increased velocities in the septal branches of patients with HCM are similar to those previously observed in tunnel-like obstructions. These findings suggest that in HCM, notwithstanding an increase in coronary flow, hemodynamically significant narrowings are present in the septal branches. Doppler TTE may become useful for evaluation of abnormal intramural coronary flow in HCM.